READ IN DATA

#VEGETAION LAYER FOR LOWER SC (INCLUDES ARUNDO)

#read in veg layer for lower Santa Clara Watershed
bios_veg_layer <- st_read(here("bios_veg_layer", "ds983.gdb")) %>% 
  filter(!st_is_empty(.)) %>% 
  clean_names()
## Reading layer `ds983' from data source 
##   `/Users/irisfoxfoot/Desktop/scr_restoration_potential/bios_veg_layer/ds983.gdb' 
##   using driver `OpenFileGDB'
## Simple feature collection with 1546 features and 23 fields
## Geometry type: MULTIPOLYGON
## Dimension:     XY
## Bounding box:  xmin: 67364.41 ymin: -422907 xmax: 120390.6 ymax: -394134
## Projected CRS: NAD83 / California Albers

Insert link to data here

#TERRESTRIAL BIODIVERSITY LAYERS FROM ACE

#terrestrial rare species
t_rare_species <- st_read(here("ACE_Summary_Datasets", "ACE_Summary_Datasets", "ds2709.gdb"))
## Reading layer `ds2709' from data source 
##   `/Users/irisfoxfoot/Desktop/scr_restoration_potential/ACE_Summary_Datasets/ACE_Summary_Datasets/ds2709.gdb' 
##   using driver `OpenFileGDB'
## Simple feature collection with 63890 features and 17 fields
## Geometry type: MULTIPOLYGON
## Dimension:     XY
## Bounding box:  xmin: -373987.9 ymin: -604495.8 xmax: 540034.3 ymax: 450023.2
## Projected CRS: NAD83 / California Albers
#terrestrial irreplaceable habitat
t_irreplaceable_habitat <- st_read(here("ACE_Summary_Datasets", "ACE_Summary_Datasets", "ds2715.gdb"))
## Reading layer `ds2715' from data source 
##   `/Users/irisfoxfoot/Desktop/scr_restoration_potential/ACE_Summary_Datasets/ACE_Summary_Datasets/ds2715.gdb' 
##   using driver `OpenFileGDB'
## Simple feature collection with 63890 features and 17 fields
## Geometry type: MULTIPOLYGON
## Dimension:     XY
## Bounding box:  xmin: -373987.9 ymin: -604495.8 xmax: 540034.3 ymax: 450023.2
## Projected CRS: NAD83 / California Albers
#....etc

Insert link to data here

#RASTER OF ARUNDO 2006 (used for extent purposes)
arundo_06 <- raster(here("arundo_05", "arundo_cov_05.tif"))

arundo_06
## class      : RasterLayer 
## dimensions : 2992, 5366, 16055072  (nrow, ncol, ncell)
## resolution : 10, 10  (x, y)
## extent     : 67134.41, 120794.4, -423477, -393557  (xmin, xmax, ymin, ymax)
## crs        : +proj=aea +lat_0=0 +lon_0=-120 +lat_1=34 +lat_2=40.5 +x_0=0 +y_0=-4000000 +datum=NAD83 +units=m +no_defs 
## source     : arundo_cov_05.tif 
## names      : arundo_cov_05 
## values     : 0, 100  (min, max)

Calculating Rare Species Score Per Polygon

In this section biodiversity data will be rasterized, clipped, etc. other small changes to initial format of data will take place here.

#CONVERT TERRESTRIAL RARE SPECIES POLYGON TO RASTER

#rasterize the polygon, using RarRankEco as the raster value
t_rare_species_raster <- fasterize(t_rare_species, arundo_06, "RarRankEco")

#plot
plot(t_rare_species_raster)

#extract terrestrial rare species score values for each veg polygon
extract_t_rare_species <- raster::extract(t_rare_species_raster, bios_veg_layer, method="simple", fun=mean, weights=TRUE, normalizeWeights=TRUE, sp = TRUE)
#convert to sf (sf makes a polygon layer like a dataframe so you can use tidyverse commands on it)
extract_t_rare_sf <- st_as_sf(extract_t_rare_species)
#fixing STUPID geometry issues with this BROKEN ASS LAYER

sf::sf_use_s2(FALSE) #updated version of the sf package causes troubles so not using it
## Spherical geometry (s2) switched off
extract_t_rare_sf %>% st_buffer(dist = 0)
## Simple feature collection with 1545 features and 24 fields
## Geometry type: POLYGON
## Dimension:     XY
## Bounding box:  xmin: 67364.41 ymin: -422907 xmax: 120390.6 ymax: -394134
## Projected CRS: NAD83 / California Albers
## First 10 features:
##                                                                    nvcsname
## 1                                                   Lepidospartum squamatum
## 2                                                                    Barren
## 3                                                         Populus fremontii
## 4                                                              Salix exigua
## 5                                       Populus trichocarpa–Salix laevigata
## 6                                                     Baccharis salicifolia
## 7       Mediterranean California naturalized annual and perennial grassland
## 8                                                                     Urban
## 9                                                                     Urban
## 10 Southwestern North American Riparian, Flooded and Swamp Forest/Scrubland
##      nvcslevel                              mapclass
## 1     Alliance               Lepidospartum squamatum
## 2         <NA>                             Riverwash
## 3     Alliance                     Populus fremontii
## 4     Alliance                          Salix exigua
## 5  Association Populus balsamifera - Salix laevigata
## 6     Alliance                 Baccharis salicifolia
## 7        Group          Non-native grasses and forbs
## 8         <NA>                             Developed
## 9         <NA>                             Developed
## 10  Macrogroup                       Riverwash scrub
##                        alliance arundo_cov tamarix   mu_source poly_number
## 1       Lepidospartum squamatum          0          Field data        6013
## 2                     Riverwash          0      No PhotoInterp           0
## 3             Populus fremontii          0      No PhotoInterp           0
## 4                  Salix exigua          0      No PhotoInterp           0
## 5           Populus balsamifera         50      No  Field data        4114
## 6         Baccharis salicifolia          0      No  Field data        4008
## 7  Non-native grasses and forbs          0      No PhotoInterp           0
## 8                     Developed          0      No PhotoInterp           0
## 9                     Developed          0      No PhotoInterp           0
## 10              Riverwash scrub          0      No PhotoInterp           0
##        uid                     calvegname calvegcode                 cwhrtype
## 1  SCR0001     Riversidean Alluvial Scrub         RS            Coastal Scrub
## 2  SCR0002                         Barren         BA                   Barren
## 3  SCR0003             Fremont Cottonwood         QF Valley Foothill Riparian
## 4  SCR0004                 Willow (shrub)         WL Valley Foothill Riparian
## 5  SCR0005               Black Cottonwood         QX         Montane Riparian
## 6  SCR0006           Baccharis (riparian)         ML Valley Foothill Riparian
## 7  SCR0007 Non-Native/Invasive Forb/Grass         IF         Annual Grassland
## 8  SCR0008      Urban/Developed (General)         UB                    Urban
## 9  SCR0009      Urban/Developed (General)         UB                    Urban
## 10 SCR0010           Riparian Mixed Shrub         NM Valley Foothill Riparian
##    cwhrcode globalrank staterank rare    cacode            nvcsalliance
## 1       CSC         G3        S3  Yes 32.070.00 Lepidospartum squamatum
## 2       BAR       <NA>      <NA> <NA>      <NA>                    <NA>
## 3       VRI         G4        S3  Yes 61.130.00       Populus fremontii
## 4       VRI         G5        S4   No 61.209.00            Salix exigua
## 5       MRI       <NA>      <NA>  Yes 61.120.09     Populus trichocarpa
## 6       VRI         G5        S4   No 63.510.00   Baccharis salicifolia
## 7       AGS       <NA>      <NA> <NA>      <NA>                    <NA>
## 8       URB       <NA>      <NA> <NA>      <NA>                    <NA>
## 9       URB       <NA>      <NA> <NA>      <NA>                    <NA>
## 10      VRI       <NA>      <NA> <NA>      <NA>                    <NA>
##                                                                 nvcsgroup
## 1                                        Mojavean semi-desert wash scrub 
## 2                                                                    <NA>
## 3  Southwestern North American riparian evergreen and deciduous woodland 
## 4                         Southwestern North American riparian/wash scrub
## 5                                 Vancouverian riparian deciduous forest 
## 6                         Southwestern North American riparian/wash scrub
## 7     Mediterranean California naturalized annual and perennial grassland
## 8                                                                    <NA>
## 9                                                                    <NA>
## 10                                                                   <NA>
##                                                                      nvcsmg
## 1                             Madrean Warm Semi-Desert Wash Woodland/Scrub 
## 2                                                                      <NA>
## 3            Southwestern North American Riparian, Flooded and Swamp Forest
## 4            Southwestern North American Riparian, Flooded and Swamp Forest
## 5              Western Cordilleran montane–boreal riparian scrub and forest
## 6            Southwestern North American Riparian, Flooded and Swamp Forest
## 7                                 California Annual and Perennial Grassland
## 8                                                                      <NA>
## 9                                                                      <NA>
## 10 Southwestern North American Riparian, Flooded and Swamp Forest/Scrubland
##         acres shape_length shape_area    layer                       geometry
## 1    2.806390     540.8866  11358.461 3.000000 POLYGON ((111742 -400401.3,...
## 2  140.228662   14133.1119 567550.453 3.603986 POLYGON ((85313.11 -402524....
## 3   13.503015    2318.2197  54651.295 3.000000 POLYGON ((96374.88 -402530....
## 4   28.799977    1818.8212 116563.347 3.000000 POLYGON ((96584.35 -402447....
## 5    7.955950    1409.3158  32200.458 3.000000 POLYGON ((96793.44 -402196....
## 6    1.914021     838.9665   7746.677 3.000000 POLYGON ((86592.05 -404044....
## 7    5.497501    1711.3135  22250.204 3.000000 POLYGON ((86308.41 -403916....
## 8   17.938057    1947.9278  72601.513 3.025759 POLYGON ((97221.06 -401983....
## 9    3.909923    1123.3439  15824.813 3.195033 POLYGON ((97240.29 -401947....
## 10   4.847574    1270.1589  19619.801 3.051057 POLYGON ((97178.42 -402045,...
#viewing
tmap_mode("view")
## tmap mode set to interactive viewing
tm_shape(extract_t_rare_species) +
    tm_polygons("layer")
## Warning in sp::proj4string(obj): CRS object has comment, which is lost in output